How to align automatically bones in edit mode and in pose mode
Bone Edit Mode and Pose Mode are two different things.

The Edit Mode functions like an automated "freeze transform" (if you are coming from Maya). This means in Edit Mode your mesh will always stay in its initial position. 
Everything you transform in Pose mode will not get changed/applied in Edit Mode. But in reverse, if you change position in Edit Mode it will be changed/applied in Pose Mode as well. 

Also keep in mind, thatin Pose Mode you have various factors, that can change the final position of your Bones. For example ik or postion constraints. Those constraints are also not active in Edit Mode. 

So long story short: there is no way to guarantee 100% synchronization between those 2 modes. But in general this dis synchronization comes from wrong setup in the bone constraints. 
Also if you want to reset all your manually set transforms in Pose Mode go to "Pose -> clear transform". 
But keep in mind "manually set" means everything you have changed by hand (with the translation and rotation tools). If there is still an active constraint that is manipulation the transform of your bone, you will not get the initial set position from Edit Mode.